Here we provide scripts we used in our study "pyTCR: a comprehensive and scalable solution for TCR-Seq data analysis to facilitate reproducibility and rigor of immunogenomics research".
Table of contents
We have compared pyTCR to the following TCR-Seq post-processing tools:
- VDJtools, https://vdjtools-doc.readthedocs.io/en/master/
- immunarch, https://immunarch.com/
We downloaded the COVID19-BWNW dataset, which was part of the ImmuneRACE Study, from ImmuneCODE™ database (https://immunerace.adaptivebiotech.com/data).
data includes the data that created all figures in the manuscript.
notebooks includes the Jupyter notebooks for all figures in the manuscript.
figures includes all of the image files for the plots generated by notebooks.
Please do not hesitate to contact us (mangul@usc.edu) if you have any comments, suggestions, or clarification requests regarding the study or if you would like to contribute to this resource.